Non-coding rna for detection of cancer

Abstract

The present disclosure relates generally to detection on non-coding RNAS molecules in a sample or diagnosis of subject based upon detection or quantification of non-coding nucleic acid sequences in a sample, specifically to identify and use of molecular biomarkers for cancer including breast cancer.

1 . A method for sequencing a ribonucleic acid (RNA) molecule from a cell-free sample, comprising:
 (a) providing said cell-free sample comprising said RNA molecule, wherein said RNA molecule comprises a non-coding sequence;   (b) subjecting said RNA molecule to reverse transcription to generate a complementary deoxyribonucleic acid (cDNA) molecule, wherein said cDNA molecule comprises a sequence corresponding to said non-coding sequence of said RNA molecule; and   (c) subjecting said cDNA molecule or derivative thereof to sequencing-by-synthesis to identify said non-coding sequence.   
     
     
         2 . The method of  claim 1 , wherein said RNA molecule is an orphan non-coding RNA (oncRNA). 
     
     
         3 . The method of  claim 1 , wherein said RNA molecule comprises T3p or functional fragment thereof. 
     
     
         4 . The method of  claim 1 , further comprising, after (a), isolating said RNA molecule from other components of said cell-free sample. 
     
     
         5 . The method of  claim 4 , wherein said isolating comprises filtration. 
     
     
         6 . The method of  claim 1 , further comprising using a result of said sequencing-by-synthesis to determine an amount of said non-coding sequence in said cell-free sample. 
     
     
         7 . The method of  claim 1 , wherein said cell-free sample comprises serum. 
     
     
         8 . The method of  claim 1 , wherein said cell-free sample comprises whole blood. 
     
     
         9 . The method of  claim 1 , wherein said cell-free sample comprises plasma. 
     
     
         10 . The method of  claim 1 , wherein said cell-free sample comprises urine. 
     
     
         11 . The method of  claim 1 , wherein said cell-free sample comprises lymph. 
     
     
         12 . The method of  claim 1 , wherein said cell-free sample comprises saliva. 
     
     
         13 . The method of  claim 1 , wherein the volume of cell-free sample is about 20 microliters to about 2 milliliters. 
     
     
         14 . The method of  claim 11 , wherein the volume of cell-free sample is about 100 microliters to about 500 microliters. 
     
     
         15 . The method of  claim 1 , wherein said sequencing-by-synthesis generates sequencing reads, which sequencing reads are processed to identify said non-coding sequence. 
     
     
         16 . The method of  claim 1 , wherein said RNA molecule has a length of less than 200 nucleotides. 
     
     
         17 . The method of  claim 13 , wherein said RNA molecule has a length between 50 and 100 nucleotides. 
     
     
         18 . The method of  claim 1 , wherein said non-coding sequence is indicative of cancer. 
     
     
         19 . The method of  claim 1 , wherein said cancer is breast cancer. 
     
     
         20 . The method  claim 1 , further comprising, after (b), amplifying said cDNA molecule.